Handle cases where the WDL workflow output contains exprs

wdl2cwl/main.py

@@ -722,7 +722,11 @@ def get_workflow_outputs(
             with WDLSourceLine(item.info, ConversionException):
                 output_name = item.name
                 item_expr = item.info.expr
-                output_source = item_expr.expr.name[::-1].replace(".", "/", 1)[::-1]
+                if isinstance(item_expr, WDL.Expr.Get):
+                    output_source = item_expr.expr.name[::-1].replace(".", "/", 1)[::-1]
+                else:
+                    output_source = f"$({self.get_expr(item_expr)})"
+
                 # replace just the last occurrence of a period with a slash
                 # by first reversing the string and the replace the first occurrence
                 # then reversing the result
@@ -1019,14 +1023,14 @@ def get_expr_get(self, wdl_get_expr: WDL.Expr.Get) -> str:
 
     def get_expr_ident(self, wdl_ident_expr: WDL.Expr.Ident) -> str:
         """Translate WDL Ident Expressions."""
-        id_name = wdl_ident_expr.name
+        id_name: str = wdl_ident_expr.name
         referee = wdl_ident_expr.referee
         optional = wdl_ident_expr.type.optional
         if referee:
             with WDLSourceLine(referee, ConversionException):
                 if isinstance(referee, WDL.Tree.Call):
                     return id_name
-                if referee.expr and (
+                if hasattr(referee, 'expr') and referee.expr is not None and (
                     wdl_ident_expr.name in self.optional_cwl_null
                     or wdl_ident_expr.name not in self.non_static_values
                 ):

wdl2cwl/tests/cwl_files/blast.cwl

@@ -0,0 +1,217 @@
+cwlVersion: v1.2
+id: blast
+class: Workflow
+requirements:
+  - class: InlineJavascriptRequirement
+inputs:
+  - id: blast_docker_override
+    type:
+      - string
+      - 'null'
+  - id: blast_docker
+    type:
+      - string
+      - 'null'
+  - id: queryfa
+    type: File
+  - id: fname
+    default: /sfs/blastdb/2019_ncov/nucl/v6/ncov
+    type: string
+  - id: method
+    default: blastn
+    type: string
+  - id: outfmt
+    default: 7
+    type: int
+  - id: evalue
+    default: 10.0
+    type: float
+  - id: Outfile
+    type:
+      - string
+      - 'null'
+  - id: threads
+    default: 8
+    type: int
+  - id: runblastp.max_target_seqs
+    default: 100
+    type: int
+  - id: runblastp.word_size
+    default: 6
+    type: int
+  - id: runblastp.seg
+    default: no
+    type: string
+  - id: runblastp.comp_based_stats
+    default: '2'
+    type: string
+  - id: runblastp.matrix
+    default: BLOSUM62
+    type: string
+  - id: runblastp.gapopen
+    default: 11
+    type: int
+  - id: runblastp.gapextend
+    default: 1
+    type: int
+  - id: runblastp.max_hsps
+    type:
+      - int
+      - 'null'
+  - id: runblastp.taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastp.negative_taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastp.lcase_masking
+    default: false
+    type: boolean
+  - id: runblastn.max_target_seqs
+    default: 100
+    type: int
+  - id: runblastn.word_size
+    default: 28
+    type: int
+  - id: runblastn.reward
+    default: 1
+    type: int
+  - id: runblastn.penalty
+    default: -2
+    type: int
+  - id: runblastn.strand
+    default: both
+    type: string
+  - id: runblastn.gapopen
+    default: 0
+    type: int
+  - id: runblastn.gapextend
+    default: 0
+    type: int
+  - id: runblastn.dust
+    default: "'20 64 1'"
+    type: string
+  - id: runblastn.max_hsps
+    type:
+      - int
+      - 'null'
+  - id: runblastn.tasks
+    default: megablast
+    type: string
+  - id: runblastn.taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastn.negative_taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastn.lcase_masking
+    default: false
+    type: boolean
+  - id: runblastx.max_target_seqs
+    default: 100
+    type: int
+  - id: runblastx.word_size
+    default: 6
+    type: int
+  - id: runblastx.seg
+    default: "'12 2.2 2.5'"
+    type: string
+  - id: runblastx.comp_based_stats
+    default: '2'
+    type: string
+  - id: runblastx.matrix
+    default: BLOSUM62
+    type: string
+  - id: runblastx.gapopen
+    default: 11
+    type: int
+  - id: runblastx.gapextend
+    default: 1
+    type: int
+  - id: runblastx.taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastx.negative_taxids
+    type:
+      - string
+      - 'null'
+  - id: runblastx.max_hsps
+    type:
+      - int
+      - 'null'
+  - id: runblastx.lcase_masking
+    default: false
+    type: boolean
+  - id: runtblastn.max_target_seqs
+    default: 100
+    type: int
+  - id: runtblastn.word_size
+    default: 6
+    type: int
+  - id: runtblastn.seg
+    default: "'12 2.2 2.5'"
+    type: string
+  - id: runtblastn.comp_based_stats
+    default: '2'
+    type: string
+  - id: runtblastn.matrix
+    default: BLOSUM62
+    type: string
+  - id: runtblastn.gapopen
+    default: 11
+    type: int
+  - id: runtblastn.gapextend
+    default: 1
+    type: int
+  - id: runtblastn.lcase_masking
+    default: false
+    type: boolean
+  - id: runtblastn.max_hsps
+    type:
+      - int
+      - 'null'
+  - id: runtblastn.taxids
+    type:
+      - string
+      - 'null'
+  - id: runtblastn.negative_taxids
+    type:
+      - string
+      - 'null'
+  - id: runtblastx.taxids
+    type:
+      - string
+      - 'null'
+  - id: runtblastx.word_size
+    default: 3
+    type: int
+  - id: runtblastx.max_target_seqs
+    default: 100
+    type: int
+  - id: runtblastx.seg
+    default: "'12 2.2 2.5'"
+    type: string
+  - id: runtblastx.matrix
+    default: BLOSUM62
+    type: string
+  - id: runtblastx.lcase_masking
+    default: false
+    type: boolean
+  - id: runtblastx.negative_taxids
+    type:
+      - string
+      - 'null'
+  - id: runtblastx.max_hsps
+    type:
+      - int
+      - 'null'
+steps: []
+outputs:
+  - id: blast.fina_output
+    outputSource: '$([inputs["runtblastx.out"] === null '
+    type: File

wdl2cwl/tests/test_cwl.py

@@ -68,6 +68,7 @@ def test_meta(caplog: pytest.LogCaptureFixture) -> None:
         ("vt.wdl"),
         ("whatshap.wdl"),
         ("workflow_inputs.wdl"),
+        ("blast.wdl"),
     ],
 )
 def test_wdls(description_name: str) -> None: